Mercurial > repos > jjohnson > find_in_reference
comparison find_in_reference.xml @ 1:856033fb26e8
Add case insensitive option
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Fri, 17 Jan 2014 14:50:53 -0600 |
| parents | fe0327a3ba81 |
| children | 30975b3ff0dc |
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| 0:fe0327a3ba81 | 1:856033fb26e8 |
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| 5 --reference "$reference" | 5 --reference "$reference" |
| 6 #if $column.set == 'yes': | 6 #if $column.set == 'yes': |
| 7 --input_column $column.input_column | 7 --input_column $column.input_column |
| 8 --reference_column $column.reference_column | 8 --reference_column $column.reference_column |
| 9 #end if | 9 #end if |
| 10 $case_insensitive | |
| 10 #if 'novel' in $outputs.__str__ or not 'found' in $outputs.__str__: | 11 #if 'novel' in $outputs.__str__ or not 'found' in $outputs.__str__: |
| 11 --output "$novel" | 12 --output "$novel" |
| 12 #end if | 13 #end if |
| 13 #if 'found' in $outputs.__str__: | 14 #if 'found' in $outputs.__str__: |
| 14 --filtered "$found" | 15 --filtered "$found" |
| 15 #end if | 16 #end if |
| 16 </command> | 17 </command> |
| 17 <inputs> | 18 <inputs> |
| 18 <param name="input" type="data" format="tabular" label="Input file to be filtered" | 19 <param name="input" type="data" format="tabular" label="Input file to be filtered" |
| 19 help="e.g. tophat junctions.bed run without GTF option or no-novel-junctions"/> | 20 help="e.g. a peptide fasta converted to tabular"/> |
| 20 <param name="reference" type="data" format="tabular" label="reference file to search" | 21 <param name="reference" type="data" format="tabular" label="reference file to search" |
| 21 help="e.g. tophat junctions.bed run with GTF option and no-novel-junctions"/> | 22 help="e.g. a protein fasta converted to tabular"/> |
| 22 <conditional name="column"> | 23 <conditional name="column"> |
| 23 <param name="set" type="select" label="select columns to compare"> | 24 <param name="set" type="select" label="select columns to compare"> |
| 24 <option value="no" selected="true">Use last column of input and reference</option> | 25 <option value="no" selected="true">Use last column of input and reference</option> |
| 25 <option value="yes">Choose the column of input and reference to compare</option> | 26 <option value="yes">Choose the column of input and reference to compare</option> |
| 26 </param> | 27 </param> |
| 30 help=""/> | 31 help=""/> |
| 31 <param name="reference_column" type="data_column" data_ref="reference" label="column in reference (defaults to last column)" | 32 <param name="reference_column" type="data_column" data_ref="reference" label="column in reference (defaults to last column)" |
| 32 help=""/> | 33 help=""/> |
| 33 </when> | 34 </when> |
| 34 </conditional> | 35 </conditional> |
| 36 <param name="case_insensitive" type="boolean" truevalue="--case_insensitive" falsevalue="" checked="false" label="Ignore case when comparing"/> | |
| 35 <param name="outputs" type="select" multiple="true" display="checkboxes" label="Choose outputs"> | 37 <param name="outputs" type="select" multiple="true" display="checkboxes" label="Choose outputs"> |
| 36 <option value="novel" selected="true">lines with no match in reference</option> | 38 <option value="novel" selected="true">lines with no match in reference</option> |
| 37 <option value="found">lines with match in reference</option> | 39 <option value="found">lines with match in reference</option> |
| 38 </param> | 40 </param> |
| 39 </inputs> | 41 </inputs> |
| 56 </test> | 58 </test> |
| 57 </tests> | 59 </tests> |
| 58 <help> | 60 <help> |
| 59 **Find in Reference** | 61 **Find in Reference** |
| 60 | 62 |
| 61 Filters lines of a tabular input file by checking if the selected input column | 63 Filters lines of a tabular input file by checking if the selected input column value |
| 62 is a substring of the selected column of any line in the reference file. | 64 is a substring of the selected column of any line in the reference file. |
| 63 | 65 |
| 64 This can be used to check if peptides sequences are present in a set of reference proteins, | 66 This can be used to check if peptides sequences are present in a set of reference proteins, |
| 65 as a means of filtering out uninteresting peptide sequences. | 67 as a means of filtering out uninteresting peptide sequences. |
| 66 | 68 |
| 69 For Example with:: | |
| 70 | |
| 71 Input | |
| 72 >pep1 LIL | |
| 73 >pep2 WTF | |
| 74 >pep3 ISK | |
| 75 | |
| 76 Reference | |
| 77 >prot1 RLET | |
| 78 >prot2 LLIL | |
| 79 >prot3 LAPSE | |
| 80 >prot3 RISKY | |
| 81 | |
| 82 The outputs | |
| 83 | |
| 84 Not found in reference | |
| 85 >pep2 WTF | |
| 86 | |
| 87 Found in reference | |
| 88 >pep1 LIL | |
| 89 >pep3 ISK | |
| 90 | |
| 91 | |
| 67 </help> | 92 </help> |
| 68 </tool> | 93 </tool> |